Many foods and herbs are experientially classified into different commodity grades in commercial circulation. Regarding the hypertoxic herb aconite, large samples are considered to be of better quality. However, this experiential classification lacks a scientific basis. In this study, we focused on the quality diversity among different grades and studied it using the minimum lethal dose assay and a novel ultra high performance liquid chromatography coupled with time-of-flight mass spectrometry method. Toxicity assay result suggested grade I aconite had the lowest toxicity (p < 0.05). Using this method with partial least squares-discriminant analysis, we discovered nine chemomarkers, including neoline, songorine, fuziline, mesaconitine, talatizidine, dexyaconitine, talatisamine, hypaconitine, and fuzitine. Considering their toxicity and activity, we found the levels of toxic ingredients hypaconitine, dexyaconitine, and mesaconitine in grade I were lower than those in grade II (p < 0.01), while the levels of efficacy ingredients songorine, talatisamine, and neoline were the highest in grade I (p < 0.01). Further study demonstrated that the quality variation was associated with plant tissue development and toxic ingredient distribution law. Our results provide scientific evidence for the experiential quality evaluation of aconite, and it will be of great utility for other foods and herbs.